MolNFT v1 · #154949 · protein

Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS W88A mutant

6KRP: “Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS W88A mutant”. X-ray diffraction, 20 pockets (best druggability 0.57). MolNFT v1 #154949 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KRP
Type: protein
Length: 2,437 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin
EC: 1.11.1.15
UniProt: Q9Y9L0
Pockets: 20 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin (EC 1.11.1.15)	protein	242	36% helix, 24% strand	Q9Y9L0
B, C, D, E, G, H, I, J	Peroxiredoxin (EC 1.11.1.15)	protein	244	34% helix, 23% strand	Q9Y9L0
F	Peroxiredoxin (EC 1.11.1.15)	protein	243	35% helix, 24% strand	Q9Y9L0

Ligands and binding sites

CIT · Citric acid · additive · 10 copies · chains A, B, I, D, C, E, F, H, G, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	314	0.57	0.76	43	CIT
2	277	0.55	0.76	36	CIT
3	288	0.55	0.76	39	CIT
4	264	0.55	0.77	43	CIT
5	279	0.55	0.76	42	CIT

Interfaces

20 interfaces between chains.

G–H · 3703 Å² buried · 53 hydrogen bonds · protein-protein
I–J · 3653 Å² buried · 51 hydrogen bonds · protein-protein
C–D · 3604 Å² buried · 48 hydrogen bonds · protein-protein
E–F · 3592 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 3591 Å² buried · 49 hydrogen bonds · protein-protein

Compared structures

6KRP · Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant · the same entry in another collection · chain J against J, TM-score 1.00
Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y9L0
Elsewhere: RCSB PDB 6KRP · PDBe 6KRP · UniProt Q9Y9L0

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